.TH g_confrms 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_confrms - fits two structures and calculates the rmsd 

.B VERSION 4.5
.SH SYNOPSIS
\f3g_confrms\fP
.BI "\-f1" " conf1.gro "
.BI "\-f2" " conf2.gro "
.BI "\-o" " fit.pdb "
.BI "\-n1" " fit1.ndx "
.BI "\-n2" " fit2.ndx "
.BI "\-no" " match.ndx "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-[no]w" ""
.BI "\-[no]one" ""
.BI "\-[no]mw" ""
.BI "\-[no]pbc" ""
.BI "\-[no]fit" ""
.BI "\-[no]name" ""
.BI "\-[no]label" ""
.BI "\-[no]bfac" ""
.SH DESCRIPTION
\&g_confrms computes the root mean square deviation (RMSD) of two
\&structures after LSQ fitting the second structure on the first one.
\&The two structures do NOT need to have the same number of atoms,
\&only the two index groups used for the fit need to be identical.
\&With \fB \-name\fR only matching atom names from the selected groups
\&will be used for the fit and RMSD calculation. This can be useful 
\&when comparing mutants of a protein.
\&


\&The superimposed structures are written to file. In a \fB .pdb\fR file
\&the two structures will be written as separate models
\&(use \fB rasmol \-nmrpdb\fR). Also in a \fB .pdb\fR file, B\-factors
\&calculated from the atomic MSD values can be written with \fB \-bfac\fR.
.SH FILES
.BI "\-f1" " conf1.gro" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-f2" " conf2.gro" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

.BI "\-o" " fit.pdb" 
.B Output
 Structure file: gro g96 pdb etc. 

.BI "\-n1" " fit1.ndx" 
.B Input, Opt.
 Index file 

.BI "\-n2" " fit2.ndx" 
.B Input, Opt.
 Index file 

.BI "\-no" " match.ndx" 
.B Output, Opt.
 Index file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-[no]one"  "no    "
 Only write the fitted structure to file

.BI "\-[no]mw"  "yes   "
 Mass\-weighted fitting and RMSD

.BI "\-[no]pbc"  "no    "
 Try to make molecules whole again

.BI "\-[no]fit"  "yes   "
 Do least squares superposition of the target structure to the reference

.BI "\-[no]name"  "no    "
 Only compare matching atom names

.BI "\-[no]label"  "no    "
 Added chain labels A for first and B for second structure

.BI "\-[no]bfac"  "no    "
 Output B\-factors from atomic MSD values

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
